Data

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Raw Data

The raw flow cytometry files have been stored on the CaltechDATA research data depository. It can be downloaded from the link below:

• Flow cytometry files (.csv) | DOI: 10.22002/D1.1241

We note that a subset of raw data files were unfortunately lost and only the preprocessed data is maintained. Please see the README file along with the raw data for more information.

Processed data

The processed data is hosted on this website and can be downloaded via the following links.

Main Text Data

• Compiled data
  Experimental fold-change measurements of mutant and wild-type strains
• Summarized data
  Experimental fold-change measurements summarized with the mean and standard error for each unique strain and IPTG concentration.
• Empirical free energy statistics
  Inferred mean fold-change, standard deviation, empirical free energy, and change in free energy.
• DNA binding energy inference statistics
  Summarized results for inference of the DNA binding energy for each DNA binding mutant strain.
• DNA binding energy inference MCMC samples
  MCMC samples from estimation of DNA binding energy for each DNA binding mutant strain.
• Inducer dissociation constant inference statistics
  Summarized results for inference of the inducer binding constants (Ka and Ki alone) for all inducer binding mutant strains.
• Inducer dissociation constant inference MCMC samples
  MCMC samples from estimation of inducer binding constants (Ka and Ki alone) for all inducer binding mutant strains.
• Allosteric parameter inference statistics
  Summarized results for inference of all allosteric parameters for the inducer binding mutant strains.
• Allosteric parameter inference MCMC samples
  MCMC samples from estimation of all allosteric parameters for inducer binding mutant strains.

Supplementary Data

• Prior predictive samples for DNA binding energy inference
• Simulation based calibration for DNA binding energy inference
• Prior predictive samples for empirical free energy inference
• Simulation based calibration for empirical free energy inference
• Simulated fold-change measurements for determining empirical free energy sensitivity limits
• Inference statistics of simulated fold-change data
• Inference statistics of empirical free energy from Razo-Mejia et al. 2018
• Prior predictive samples for inference of allosteric parameters
• Simulation based calibration for inference of allosteric parameters
• Global DNA binding energy inference MCMC samples
• Global DNA binding energy inference statistics
• Global allosteric parameter inference MCMC samples
• Global allosteric parameter inference statistics

Auxiliary Data Files

• Fold-change measurements from Razo-Mejia et al. 2018
• Combined fold-change measurements from Garcia & Phillips 2011 and Brewster et al. 2014